Greetings fellow Paladins (for I swear to the Cavalier)! Did your alignment actually change after the fight (i.e. did you see [character name]-lost class - Undead Hunter) or did you only notice it after the fight? It could be that you have chosen dialogue options that are interpreted as evil. Make sure that when speaking to NPC's you always say the noble thing.
There is another possibility however, detailed below:
SPOILERS: Re the end of SoA
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You might have changed alignments in the tests in hell at the end of SoA. In each of these test you must do the noble thing and make sacrifices. If you do not your alignment becomes Neutral/Evil. That's the only place that's cropped up a lot as far as alignment changes are concerned. If it's happened later then this though, I'm really not sure what's occurred. I too had no problems after killing Gromnir.
It's possible you've been hit by some sort of bug.
The best advice I can give you is to go back to a previous save game and try some different dialogue options. Sorry I couldn't be of any more help.
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"Our deepest fear is not that we are inadequate.
Our deepest fear is that we are powerful beyond measure."